Import Data

Import Genome File

The genome data can be used to generate karyotype data for circos plotting and draw snail plot.

Go to File menu -> Import Data -> Import Genome File… to select a FASTA formatted genome file (gzip compressed genome file supported). The imported genome data has five columns: id, chrom, length, gc, ns.

The description of columns in genome data

Column

Description

id

chromosome id generated by circhart

chrom

chromosome name

length

total number of bases

gc

GC contents

ns

number of unknown bases
_images/genome_data.png

View of imported genome data

Note

The imported genome data will be assigned data type of genome.

Import Genome Annotation

The annotation data can be used to prepare circos plot data.

Go to File menu -> Import Data -> Import Genome Annotation to select a GTF or GFF file to import. The GTF or GFF file can be gzip compressed.

_images/gxf_data.png

View of imported annotation data

Note

The entire annotation file will not be loaded into circhart. It will read the first 1000 lines to get feature and attribution information. The imported data will be assigned data type of annotation.

Import Genome Bands

The genome bands can be used to prepare band data for circos plotting. Not all species have genome bands. You can go to UCSC to download genome bands.

  1. Go to UCSC Genome Table Browser.

    _images/bands.png

    UCSC Genome Table Browser

  2. Select a genome and assembly you desired.

  3. Select Mapping and Sequencing for Group.

  4. Select Cytobands (Ideogram) or Chromosome Band (Ideogram) for Track.

  5. Input output filename

  6. Click Get output button to download genome bands.

  7. Go to File menu -> Import Data -> Import Genome Bands… to select downloaded bands file.

The imported genome bands has five columns: chrom, start, end, name, stain.

The description of columns in genome bands

Column

Description

id

uniq id generated by circhart

chrom

chromosome name

start

start position

end

end position

stain

stain color name
_images/genome_band.png

View of genome bands

Import Genome Variations

The genome variation data can be used to prepare circos plot data.

Go to File menu -> Import Data -> Import Genome Variations to select a VCF file to import variations. The VCF file can be gzip format.

_images/vcf_data.png

View of imported variation data

Note

Similarly, Circhart will read the first 1000 lines. The imported data will be assigned data type of variations.

Import Genome Regions

The genome region data can be used to prepare circos plot data. The genome region data is generally stored as BED format.

Go to File menu -> Import Data -> Import Genome Regions to select a BED file to import regions. The BED file can be gzip format.

_images/bed_data.png

View of imported bed data

Note

Similarly, Circhart will read the first 1000 lines. The imported data will be assigned data type of regions.

Import collinearity file

The collinearity file is the result of synteny analysis generally generated by MCScanX and can be used to prepare link data for circos plotting.

The collinearity file contains contents like this:

############### Parameters ###############
# MATCH_SCORE: 50
# MATCH_SIZE: 5
# GAP_PENALTY: -1
# OVERLAP_WINDOW: 5
# E_VALUE: 1e-05
# MAX GAPS: 25
############### Statistics ###############
# Number of collinear genes: 647, Percentage: 2.91
# Number of all genes: 22209
##########################################
## Alignment 0: score=314.0 e_value=1.6e-07 N=7 em01&em01 plus
  0-  0:        EMA01G00523.1   EMA01G03472.1         0
  0-  1:        EMA01G00527.1   EMA01G03477.1    1e-138
  0-  2:        EMA01G00530.1   EMA01G03478.1     4e-88
  0-  3:        EMA01G00534.1   EMA01G03481.1         0
  0-  4:        EMA01G00535.1   EMA01G03482.1         0
  0-  5:        EMA01G00542.1   EMA01G03487.1    4e-113
  0-  6:        EMA01G00543.1   EMA01G03509.1         0
## Alignment 1: score=316.0 e_value=1.7e-09 N=7 em01&em02 plus
  1-  0:        EMA01G02065.1   EMA02G01577.1     3e-40
  1-  1:        EMA01G02067.1   EMA02G01579.1     1e-21
  1-  2:        EMA01G02072.1   EMA02G01583.1         0
  1-  3:        EMA01G02081.1   EMA02G01586.1         0
  1-  4:        EMA01G02101.1   EMA02G01593.1     4e-43
  1-  5:        EMA01G02103.1   EMA02G01594.1    4e-109
  1-  6:        EMA01G02105.1   EMA02G01595.1     1e-46
## Alignment 2: score=542.0 e_value=3.3e-24 N=12 em01&em02 minus
  2-  0:        EMA01G01974.1   EMA02G01686.1     6e-60
  2-  1:        EMA01G02000.1   EMA02G01682.1     1e-62
  2-  2:        EMA01G02013.1   EMA02G01677.1    2e-167
  2-  3:        EMA01G02014.1   EMA02G01676.1     1e-67
  2-  4:        EMA01G02018.1   EMA02G01673.1     5e-19
  2-  5:        EMA01G02019.1   EMA02G01671.1     4e-28
  2-  6:        EMA01G02022.1   EMA02G01669.1     3e-41
  2-  7:        EMA01G02023.1   EMA02G01667.1     7e-78
  2-  8:        EMA01G02025.1   EMA02G01663.1     1e-86
  2-  9:        EMA01G02027.1   EMA02G01660.1     2e-59
  2- 10:        EMA01G02032.1   EMA02G01650.1    2e-121
  2- 11:        EMA01G02033.1   EMA02G01649.1     2e-60
## Alignment 3: score=269.0 e_value=1.7e-06 N=6 em01&em03 minus
  3-  0:        EMA01G02962.1   EMA03G02081.1         0
  3-  1:        EMA01G02963.1   EMA03G02068.1     9e-18
  3-  2:        EMA01G02966.1   EMA03G02066.1         0
  3-  3:        EMA01G02969.1   EMA03G02064.1         0
  3-  4:        EMA01G02972.1   EMA03G02058.1     3e-29

Go to File menu -> Import Data -> Import Collinearity File to select a collinearity file to import.

_images/collinearity.png

View of collinearity data